Contacts of the helix formed by residues 367 - 377 (chain D) in PDB entry 1MPX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 367 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300D MSE 3.8 25.1 - - + -
334D VAL* 5.0 2.7 - - + -
363D PHE* 3.0 24.5 + - + +
365D HIS 3.5 0.2 - - - -
366D ASP* 1.3 86.9 - - + +
368D LEU* 1.3 66.5 + - - +
369D ARG 3.5 1.3 - - - -
370D PRO* 3.5 2.8 - - - +
371D PHE* 3.2 24.6 + - - +
385D THR* 4.4 11.8 + - + +
386D PRO* 4.4 14.8 - - + -
389D PHE* 3.8 41.5 - - + -
400D ARG* 4.6 5.6 - - - +
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Residues in contact with LEU 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D GLY 5.4 0.4 - - - +
106D VAL* 4.3 11.9 - - + -
107D PHE* 4.0 18.4 - - + -
171D ILE* 3.8 24.5 - - + -
195D VAL* 3.7 30.1 - - + -
197D GLU* 4.8 0.9 - - - +
300D MSE 4.8 3.4 - - - -
344D ASN* 6.2 0.4 - - - +
363D PHE* 2.9 39.7 + - + +
364D ARG* 3.4 20.0 - - + +
367D VAL* 1.3 75.6 - - - +
369D ARG* 1.3 65.1 + - - +
371D PHE* 3.3 5.3 + - + +
372D PHE* 3.0 33.0 + - + +
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Residues in contact with ARG 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D VAL* 3.5 32.4 + - + -
107D PHE* 5.8 1.8 - - - -
109D GLU* 4.2 15.8 + - - +
110D GLY* 3.4 34.3 + - - +
112D TYR* 4.3 4.7 - - - -
364D ARG 3.0 19.4 + - - +
365D HIS* 3.7 16.0 + - + +
368D LEU* 1.3 75.9 - - - +
370D PRO* 1.3 67.1 - - + +
372D PHE* 3.3 5.5 + - - +
373D ASP* 2.9 66.4 + - - +
377D VAL* 6.1 0.6 - - - +
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Residues in contact with PRO 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D HIS 3.4 13.7 - - - +
366D ASP* 3.5 17.7 - - - +
367D VAL* 3.5 11.9 - - - +
369D ARG* 1.3 97.8 - - + +
371D PHE* 1.3 60.1 + - - +
373D ASP* 3.7 8.3 - - + +
374D GLN* 3.0 19.8 + - - +
381D PRO 5.0 0.9 - - - +
383D ALA* 3.4 29.0 - - + +
384D ASP 5.6 0.4 - - - +
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Residues in contact with PHE 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D VAL* 3.3 28.9 - - + +
194D ALA 4.4 1.6 - - - -
195D VAL* 4.2 5.6 - - + -
298D PRO* 4.0 16.8 - - + -
300D MSE 3.7 38.4 - - + -
332D TYR* 3.7 35.2 - + - -
367D VAL 3.2 19.4 + - - +
368D LEU* 3.5 4.5 - - + +
369D ARG 3.3 0.2 - - - -
370D PRO* 1.3 78.3 - - - +
372D PHE* 1.3 69.4 + + - +
374D GLN* 3.7 6.1 + - - +
375D TYR* 3.3 44.6 - + - -
383D ALA* 4.0 2.2 - - - +
385D THR* 3.7 26.9 - - + +
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Residues in contact with PHE 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D VAL* 3.8 21.5 - - + -
107D PHE* 3.5 31.0 - + + -
112D TYR* 3.3 11.9 - + + +
169D GLY* 4.1 3.6 - - - -
170D MSE 3.8 25.1 - - - -
171D ILE* 4.3 6.1 - - + -
193D VAL* 3.6 26.7 - - + -
195D VAL* 3.5 26.9 - - + -
368D LEU* 3.0 27.3 + - + +
369D ARG* 3.7 3.4 - - - +
371D PHE* 1.3 77.6 - + - +
373D ASP* 1.3 60.5 + - - +
375D TYR* 3.3 2.8 + - - -
376D LEU* 2.9 55.0 + - + +
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Residues in contact with ASP 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D TYR* 2.5 32.0 + - - -
369D ARG* 2.9 58.9 + - - +
370D PRO* 3.7 8.7 - - + +
372D PHE* 1.3 76.1 - - - +
374D GLN* 1.3 63.8 - - - +
377D VAL* 3.0 34.4 + - + +
380D ALA* 3.1 20.5 - - + +
381D PRO* 5.8 2.0 - - + +
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Residues in contact with GLN 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D PRO 3.0 16.4 + - - +
371D PHE* 3.7 8.5 - - - +
372D PHE 3.2 0.4 - - - -
373D ASP* 1.3 78.7 - - - +
375D TYR* 1.3 93.1 + - + +
377D VAL 4.6 4.5 - - - +
380D ALA* 4.2 8.6 - - - +
381D PRO 3.9 21.8 - - - +
382D LYS* 4.2 12.8 - - - +
383D ALA* 3.0 32.4 + - - +
385D THR* 4.6 3.3 + - - -
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Residues in contact with TYR 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D LYS* 3.8 8.0 - - - +
192D LYS* 3.4 40.9 - - + +
193D VAL* 4.1 14.1 - - + -
298D PRO* 3.5 35.5 - - + +
329D THR* 3.5 22.7 + - - -
330D LEU* 5.4 1.1 - - + +
332D TYR* 5.0 2.6 + - - -
371D PHE* 3.3 37.3 - + - -
372D PHE 3.3 4.4 + - - +
373D ASP 3.2 0.2 - - - -
374D GLN* 1.3 107.3 + - + +
376D LEU* 1.3 60.4 + - - +
377D VAL 4.0 0.4 - - - -
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Residues in contact with LEU 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D PRO* 3.5 16.2 - - + +
75D ILE 4.6 2.7 - - - +
112D TYR* 3.7 15.3 - - + -
165D ASN* 2.8 26.3 + - - -
167D LYS* 3.6 14.0 - - + +
168D VAL 3.4 38.1 - - - +
169D GLY* 3.7 6.5 - - - +
192D LYS* 3.9 9.6 - - + -
193D VAL* 3.6 13.5 - - + -
372D PHE* 2.9 50.4 + - + +
375D TYR* 1.3 86.6 - - - +
377D VAL* 1.3 61.5 + - - +
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Residues in contact with VAL 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D ASN 6.1 0.2 - - - -
74D PRO* 4.0 17.3 - - + -
110D GLY 5.1 5.4 - - - +
112D TYR* 3.8 12.6 - - + +
165D ASN* 4.6 0.9 - - - +
167D LYS* 4.6 2.6 + - - -
369D ARG* 6.1 0.4 - - - +
373D ASP* 3.0 39.2 + - + +
374D GLN 4.6 3.8 - - - +
375D TYR 5.4 0.3 - - - -
376D LEU* 1.3 78.4 - - - +
378D ASP* 1.3 76.1 + - + +
379D GLY 3.3 0.9 + - - -
380D ALA* 3.2 26.1 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il